RetrogeneDB ID: retro_slyc_21

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 12:36842792..36843941(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc12g049430.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc07g066420.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_21
ATGTCTGTCATGATTGTAACAAGTTTGGGGGATATGGTAATTGATTTGTTTACCGATGAATGTCCTTTGACATGCAAAAA
TTTTCTTAAATTATGCAAGATAAAATACTATCATAATTGTCTATTACATACCGTTCGGAAGAACTTCACCATGCAAACGG
GAGATCCAACTGGAACAGGATCCGGAGGAGATTCGATATACAAATTTCTATACGGGAGTCAAGCTCGTTTTTTTGGAGAT
GAGATTCATCCACGCCTGAAGCATTCAAAGAAGGGAACGGTTGCCATGTCTAGCACTGGTATTGGTGAGAAGAATCTAAA
TGCTTCCCAGTTTTATATCACGTTACGTGATGATCTAGACTCACTTGATGGACAGCATACTGTTTTCGGAGAGATTACAG
AAGGGTTTGACACGCTAAATAGGATCAATGAAGCTTATGTCGATGACAAGGGCAAGCCTCATCAAAATATACGAATCAAA
CACACTTACCTATTGTATGATCCTTTCGATGATCCTTCCCAGTTAGAAGACTTGATTCCAGATGCTTCACCTGAAAGAAA
GCCGGAAGATGAGATTGATGATGATGATGATGTTCGACTAGAGGATGATTGGACGCCAAAGGATGAGGAATTAGGTGTTG
GTGAAGAGAAGGAAGCACACTCCCGAGCAGTAATACTTGAAAGTGTAGGAGACATTCCTGATGCTGAGATGAAACCCCCT
GAGAATGTGCTCTTTGTTTGTAAATTAAATCCCTCAACTGAAGAGGAAGCACTCTATATAATCTTCTCATGCTTTGGAAC
CGTGACATCTGTTGAAATTATCAGAGATCACAAGACTGGGGATAGCCATTGTTATGCTTTTATCGAGTTCGAGGACAAGG
AGTCATGCGAGCAAGCATATTTTAAGATGGATAATACTAAAATTGATGATCGAAGGATACGAGTTGATTTTAGTCAGAGT
GTAGCAAAGTTATGGTCCCAATATCGACCTAGAACTCAAAGAGGCAGTGGTGTTGATGCCTTCAAAGAAGACAAGAAGCA
GCATGGTGGACATTGCAACTCAAAGTACACTAAATTTCTGAAAACAAGAAAAGAGACAAGAAATCACAAAGAAAGAAAAC
ACCGGCAAATAACAAAGAAGACACGTTAA

Alignment

ORF - retro_slyc_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.86 %
• Parental protein coverage: 59.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVMIVTSLGEIVIDLFTDRCPLTCKNFLKLCKIKYYNGCLFHTIQKDFTAQTGDPTGTGSGGDSVYKIL
          MSVMIVTSLG..VIDLFTD.CPLTCKNFLKLCKIKYY..CL.HT..K.FT.QTGDPTGTGSGGDS.YK.L
Retrocopy MSVMIVTSLGDMVIDLFTDECPLTCKNFLKLCKIKYYHNCLLHTVRKNFTMQTGDPTGTGSGGDSIYKFL

Parental  YGDQARFFGDEIHLDLKHSKMGTVAMASAG---ENLNASQFYITLRDDLDYLDGKHTVFGEMAEGQETLD
          YG.QARFFGDEIH..LKHSK.GTVAM.S.G....NLNASQFYITLRDDLD.LDG.HTVFGE..EG..TL.
Retrocopy YGSQARFFGDEIHPRLKHSKKGTVAMSSTGIGEKNLNASQFYITLRDDLDSLDGQHTVFGEITEGFDTLN

Parental  RINEAYVDGKGRPFKNIRIKHTYILDDPFDDPPQLSELVPDASPEGKPKDEVEDDVRLEDDWVPMDEQLG
          RINEAYVD.KG.P..NIRIKHTY.L.DPFDDP.QL..L.PDASPE.KP.DE..D.....DD....D....
Retrocopy RINEAYVDDKGKPHQNIRIKHTYLLYDPFDDPSQLEDLIPDASPERKPEDEIDD----DDDVRLEDDWTP

Parental  MQELEEVLRAKEAHSRAVVLESVGDIPDAEIKPPDNVLFVCKLNPVTEDEDLYTIFSRFGTVTSAEIIRD
          ..E...V...KEAHSRAV.LESVGDIPDAE.KPP.NVLFVCKLNP.TE.E.LY.IFS.FGTVTS.EIIRD
Retrocopy KDEELGVGEEKEAHSRAVILESVGDIPDAEMKPPENVLFVCKLNPSTEEEALYIIFSCFGTVTSVEIIRD

Parental  FKTGDSLCYAFIEFEDKEACEQAYFKMDNALIDDRRIHVDFSQSVAKLWSQYRRKDQTGKGRGCFKCGSL
          .KTGDS.CYAFIEFEDKE.CEQAYFKMDN..IDDRRI.VDFSQSVAKLWSQYR...Q.G.G...FK....
Retrocopy HKTGDSHCYAFIEFEDKESCEQAYFKMDNTKIDDRRIRVDFSQSVAKLWSQYRPRTQRGSGVDAFKEDKK

Parental  DH
          .H
Retrocopy QH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Solanum lycopersicum was not studied using RNA-Seq expression data.

ChIP-Seq

Solanum lycopersicum was not studied using ChIP-Seq data.

EST

Solanum lycopersicum was not studied using EST data.

TSS

Solanum lycopersicum was not studied using FANTOM5 data.

Lab

retro_slyc_21 was not experimentally validated.

Homology

Retrocopy orthology:

Solanum lycopersicum does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum lycopersicum	Solyc07g066420.2	1 retrocopy	retro_slyc_21 ,